Our objective is to investigate the role of human breast milk and artificial formula in the recruitment, assembly, structuring and functioning of microbial communities in the premature gut. We hypothesize that the distinct intestinal chemical environment created by diet sets a trajectory towards establishment of microbial communities that differ between breast milk and formula fed infants thus explaining the protective effect of breast milk against microbe-mediated neonatal diseases, such as necrotizing enterocolitis. Enhancing our understanding of the relationship between diet and the succession of neonatal gut microbiota may eventually allow us to develop novel strategies to precisely manipulate the gut microbiota in order to control disease incidence and outcome. The basic study protocol involves daily stool sampling and molecular analysis of intestinal neonatal microbiota during the first few weeks following birth. This study protocol will allow us to track diet dependent succession of species leading to the establishment of distinct microbial assemblages in a high temporal resolution. We will use these colonization data to identify stable states of microbial communities for which we can use metagenomic techniques to study adaptation to the diet-dependent environment. Metagenomic data will also be used to compare the virulence potential of microbial communities. Finally, we will determine the metabolic footprint of major bacterial taxa and predict which metabolites have the potential to inhibit or enhance the bloom of each taxon. For each individual host, we will identify several time points when new species enter the intestinal ecosystem; these time points will be foci for metabolomic analyses to determine the flux of chemical components associated with species introductions. PUBLIC HEALTH RELEVANCE: Our objective is to investigate the role of human breast milk and artificial formula diets in the establishment of the neonatal gut microbiota. Serial stool samples will be used to study diet dependent microbial community dynamics and functional properties of microbiota from formula fed and milk fed neonates. We propose to determine a metabolic footprint of major bacterial taxa and suggest which metabolites are potentially able to inhibit or enhance the bloom of each taxon using a metabolomics approach.